FMO DATABASE

FMODB ID: VRL71

Calculation Name: 2Z99-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2Z99

Chain ID: A

ChEMBL ID:

UniProt ID: O33209

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	160
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1213892.959896
FMO2-HF: Nuclear repulsion	1153395.659535
FMO2-HF: Total energy	-60497.300361
FMO2-MP2: Total energy	-60675.876623

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:21:ALA)

Summations of interaction energy for fragment #1(A:21:ALA)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-1.274	1.453	-0.03	-1.43	-1.268	0.003

Interaction energy analysis for fragmet #1(A:21:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : 0.000

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	23	LEU	0	-0.024	0.003	3.814	-0.405	2.151	-0.029	-1.411	-1.117	0.003
4	A	24	ASP	-1	-0.840	-0.928	6.803	-0.537	-0.537	0.000	0.000	0.000	0.000
5	A	25	ALA	0	-0.036	-0.033	10.117	0.009	0.009	0.000	0.000	0.000	0.000
6	A	26	ASP	-1	-0.844	-0.926	13.353	-0.274	-0.274	0.000	0.000	0.000	0.000
7	A	27	GLU	-1	-0.869	-0.909	8.501	-0.230	-0.230	0.000	0.000	0.000	0.000
8	A	28	LEU	0	-0.021	-0.006	9.131	0.069	0.069	0.000	0.000	0.000	0.000
9	A	29	LYS	1	0.854	0.904	10.676	0.340	0.340	0.000	0.000	0.000	0.000
10	A	30	ARG	1	0.838	0.905	12.105	0.308	0.308	0.000	0.000	0.000	0.000
11	A	31	VAL	0	0.016	0.012	8.040	0.074	0.074	0.000	0.000	0.000	0.000
12	A	32	LEU	0	0.010	-0.017	11.514	0.059	0.059	0.000	0.000	0.000	0.000
13	A	33	GLU	-1	-0.884	-0.926	14.196	-0.193	-0.193	0.000	0.000	0.000	0.000
14	A	34	ALA	0	-0.031	-0.013	13.872	0.035	0.035	0.000	0.000	0.000	0.000
15	A	35	LEU	0	-0.006	-0.014	11.682	0.031	0.031	0.000	0.000	0.000	0.000
16	A	36	LEU	0	-0.037	-0.026	15.974	0.027	0.027	0.000	0.000	0.000	0.000
17	A	37	LEU	0	-0.067	-0.021	18.750	0.023	0.023	0.000	0.000	0.000	0.000
18	A	38	VAL	0	-0.019	-0.015	17.838	0.018	0.018	0.000	0.000	0.000	0.000
19	A	39	ILE	0	-0.058	0.002	19.394	0.010	0.010	0.000	0.000	0.000	0.000
20	A	40	ASP	-1	-0.844	-0.929	22.009	-0.086	-0.086	0.000	0.000	0.000	0.000
21	A	41	THR	0	-0.034	-0.029	24.497	0.012	0.012	0.000	0.000	0.000	0.000
22	A	42	PRO	0	-0.077	-0.025	23.793	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	43	VAL	0	0.062	0.049	18.622	0.001	0.001	0.000	0.000	0.000	0.000
24	A	44	THR	0	0.027	0.006	19.157	0.002	0.002	0.000	0.000	0.000	0.000
25	A	45	ALA	0	0.030	0.012	17.657	-0.026	-0.026	0.000	0.000	0.000	0.000
26	A	46	ASP	-1	-0.827	-0.913	15.751	-0.455	-0.455	0.000	0.000	0.000	0.000
27	A	47	ALA	0	-0.009	0.009	14.863	-0.047	-0.047	0.000	0.000	0.000	0.000
28	A	48	LEU	0	0.006	0.006	14.000	-0.029	-0.029	0.000	0.000	0.000	0.000
29	A	49	ALA	0	-0.027	-0.017	11.849	-0.085	-0.085	0.000	0.000	0.000	0.000
30	A	50	ALA	0	0.005	-0.008	10.252	-0.182	-0.182	0.000	0.000	0.000	0.000
31	A	51	ALA	0	-0.040	-0.015	9.721	-0.082	-0.082	0.000	0.000	0.000	0.000
32	A	52	THR	0	-0.064	-0.044	7.366	0.100	0.100	0.000	0.000	0.000	0.000
33	A	53	GLU	-1	-0.951	-0.958	4.391	-2.279	-2.108	-0.001	-0.019	-0.151	0.000
34	A	54	GLN	0	-0.054	-0.021	6.000	0.053	0.053	0.000	0.000	0.000	0.000
35	A	55	PRO	0	0.003	-0.005	9.019	0.283	0.283	0.000	0.000	0.000	0.000
36	A	56	VAL	0	0.094	0.023	12.407	0.018	0.018	0.000	0.000	0.000	0.000
37	A	57	TYR	0	-0.020	-0.006	14.343	0.029	0.029	0.000	0.000	0.000	0.000
38	A	58	ARG	1	0.890	0.954	9.720	1.461	1.461	0.000	0.000	0.000	0.000
39	A	59	VAL	0	0.044	0.023	12.482	0.056	0.056	0.000	0.000	0.000	0.000
40	A	60	ALA	0	-0.020	-0.016	15.019	0.069	0.069	0.000	0.000	0.000	0.000
41	A	61	ALA	0	0.006	0.003	18.090	0.048	0.048	0.000	0.000	0.000	0.000
42	A	62	LYS	1	0.898	0.960	14.843	0.472	0.472	0.000	0.000	0.000	0.000
43	A	63	LEU	0	0.025	0.009	17.292	0.048	0.048	0.000	0.000	0.000	0.000
44	A	64	GLN	0	-0.001	-0.005	19.375	0.046	0.046	0.000	0.000	0.000	0.000
45	A	65	LEU	0	-0.016	0.015	19.530	0.019	0.019	0.000	0.000	0.000	0.000
46	A	66	MET	0	-0.033	-0.001	17.368	0.006	0.006	0.000	0.000	0.000	0.000
47	A	67	ALA	0	-0.033	-0.017	21.216	0.030	0.030	0.000	0.000	0.000	0.000
48	A	68	ASP	-1	-0.857	-0.939	24.333	-0.206	-0.206	0.000	0.000	0.000	0.000
49	A	69	GLU	-1	-0.890	-0.967	20.783	-0.270	-0.270	0.000	0.000	0.000	0.000
50	A	70	LEU	0	-0.068	-0.031	23.354	0.025	0.025	0.000	0.000	0.000	0.000
51	A	71	THR	0	-0.032	-0.019	26.601	0.020	0.020	0.000	0.000	0.000	0.000
52	A	72	GLY	0	0.011	0.022	28.564	0.010	0.010	0.000	0.000	0.000	0.000
53	A	73	ARG	1	0.879	0.937	25.068	0.146	0.146	0.000	0.000	0.000	0.000
54	A	74	ASP	-1	-0.869	-0.917	30.823	-0.090	-0.090	0.000	0.000	0.000	0.000
55	A	75	SER	0	-0.030	-0.011	27.136	0.013	0.013	0.000	0.000	0.000	0.000
56	A	76	GLY	0	0.043	0.021	30.139	0.002	0.002	0.000	0.000	0.000	0.000
57	A	77	ILE	0	-0.022	-0.017	24.938	0.003	0.003	0.000	0.000	0.000	0.000
58	A	78	ASP	-1	-0.795	-0.904	27.904	-0.155	-0.155	0.000	0.000	0.000	0.000
59	A	79	LEU	0	-0.010	0.018	20.834	0.007	0.007	0.000	0.000	0.000	0.000
60	A	80	ARG	1	0.879	0.929	25.229	0.134	0.134	0.000	0.000	0.000	0.000
61	A	81	HIS	0	-0.029	-0.022	24.723	-0.014	-0.014	0.000	0.000	0.000	0.000
62	A	82	THR	0	-0.012	-0.019	26.342	0.015	0.015	0.000	0.000	0.000	0.000
63	A	83	SER	0	0.012	0.013	26.964	-0.011	-0.011	0.000	0.000	0.000	0.000
64	A	84	GLU	-1	-0.915	-0.967	27.116	-0.144	-0.144	0.000	0.000	0.000	0.000
65	A	85	GLY	0	-0.014	-0.016	23.492	-0.010	-0.010	0.000	0.000	0.000	0.000
66	A	86	TRP	0	-0.006	-0.006	20.847	0.013	0.013	0.000	0.000	0.000	0.000
67	A	87	ARG	1	0.909	0.950	22.569	0.128	0.128	0.000	0.000	0.000	0.000
68	A	88	MET	0	0.010	0.015	21.355	0.000	0.000	0.000	0.000	0.000	0.000
69	A	89	TYR	0	-0.004	-0.005	25.086	0.013	0.013	0.000	0.000	0.000	0.000
70	A	90	THR	0	0.035	0.023	28.899	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	91	ARG	1	0.810	0.900	29.118	0.134	0.134	0.000	0.000	0.000	0.000
72	A	92	ALA	0	0.054	0.013	33.013	0.007	0.007	0.000	0.000	0.000	0.000
73	A	93	ARG	1	0.902	0.934	36.511	0.085	0.085	0.000	0.000	0.000	0.000
74	A	94	PHE	0	-0.022	-0.008	33.958	0.006	0.006	0.000	0.000	0.000	0.000
75	A	95	ALA	0	0.043	0.027	37.492	0.003	0.003	0.000	0.000	0.000	0.000
76	A	96	PRO	0	0.025	0.007	38.791	0.004	0.004	0.000	0.000	0.000	0.000
77	A	97	TYR	0	-0.031	-0.021	38.157	0.003	0.003	0.000	0.000	0.000	0.000
78	A	98	VAL	0	0.007	0.009	34.896	0.003	0.003	0.000	0.000	0.000	0.000
79	A	99	GLU	-1	-0.935	-0.976	37.878	-0.047	-0.047	0.000	0.000	0.000	0.000
80	A	100	LYS	1	0.908	0.950	41.193	0.048	0.048	0.000	0.000	0.000	0.000
81	A	101	LEU	0	0.024	0.026	36.197	0.003	0.003	0.000	0.000	0.000	0.000
82	A	102	LEU	0	0.006	0.004	35.953	0.003	0.003	0.000	0.000	0.000	0.000
83	A	103	LEU	0	0.042	0.019	39.926	0.004	0.004	0.000	0.000	0.000	0.000
84	A	104	ASP	-1	-0.947	-0.951	42.682	-0.028	-0.028	0.000	0.000	0.000	0.000
85	A	105	GLY	0	-0.080	-0.043	42.058	0.002	0.002	0.000	0.000	0.000	0.000
86	A	106	ALA	0	-0.068	-0.034	43.049	0.002	0.002	0.000	0.000	0.000	0.000
87	A	107	ARG	1	0.855	0.930	45.647	0.025	0.025	0.000	0.000	0.000	0.000
88	A	108	THR	0	0.097	0.059	45.728	0.000	0.000	0.000	0.000	0.000	0.000
89	A	109	LYS	1	1.000	0.998	47.832	0.009	0.009	0.000	0.000	0.000	0.000
90	A	110	LEU	0	-0.013	0.001	49.820	0.000	0.000	0.000	0.000	0.000	0.000
91	A	111	THR	0	0.065	0.020	53.179	0.001	0.001	0.000	0.000	0.000	0.000
92	A	112	ARG	1	1.024	0.999	54.754	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	113	ALA	0	0.028	0.022	57.367	0.000	0.000	0.000	0.000	0.000	0.000
94	A	114	ALA	0	0.015	-0.008	57.114	0.000	0.000	0.000	0.000	0.000	0.000
95	A	115	LEU	0	0.026	0.010	55.255	0.000	0.000	0.000	0.000	0.000	0.000
96	A	116	GLU	-1	-0.846	-0.914	59.488	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	117	THR	0	-0.015	-0.017	62.546	0.000	0.000	0.000	0.000	0.000	0.000
98	A	118	LEU	0	-0.020	-0.001	59.142	0.000	0.000	0.000	0.000	0.000	0.000
99	A	119	ALA	0	0.034	0.012	63.004	0.000	0.000	0.000	0.000	0.000	0.000
100	A	120	VAL	0	-0.054	-0.019	64.887	0.000	0.000	0.000	0.000	0.000	0.000
101	A	121	VAL	0	0.001	-0.004	66.087	0.000	0.000	0.000	0.000	0.000	0.000
102	A	122	ALA	0	0.012	0.017	65.084	0.000	0.000	0.000	0.000	0.000	0.000
103	A	123	TYR	0	-0.030	-0.021	66.084	0.000	0.000	0.000	0.000	0.000	0.000
104	A	124	ARG	1	0.881	0.948	70.039	0.005	0.005	0.000	0.000	0.000	0.000
105	A	125	GLN	0	0.029	-0.005	67.892	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	126	PRO	0	0.042	0.035	71.447	0.000	0.000	0.000	0.000	0.000	0.000
107	A	127	VAL	0	-0.044	0.002	70.522	0.001	0.001	0.000	0.000	0.000	0.000
108	A	128	THR	0	0.069	0.043	72.308	0.000	0.000	0.000	0.000	0.000	0.000
109	A	129	ARG	1	0.918	0.922	66.389	0.010	0.010	0.000	0.000	0.000	0.000
110	A	130	ALA	0	0.005	0.011	71.142	0.001	0.001	0.000	0.000	0.000	0.000
111	A	131	ARG	1	0.998	0.997	73.989	0.006	0.006	0.000	0.000	0.000	0.000
112	A	132	VAL	0	-0.001	0.005	67.356	0.001	0.001	0.000	0.000	0.000	0.000
113	A	133	SER	0	-0.044	-0.046	69.471	0.000	0.000	0.000	0.000	0.000	0.000
114	A	134	ALA	0	0.006	0.004	70.514	0.001	0.001	0.000	0.000	0.000	0.000
115	A	135	VAL	0	-0.055	-0.033	70.309	0.001	0.001	0.000	0.000	0.000	0.000
116	A	136	ARG	1	0.837	0.914	62.653	0.004	0.004	0.000	0.000	0.000	0.000
117	A	137	GLY	0	0.016	0.028	68.523	0.001	0.001	0.000	0.000	0.000	0.000
118	A	138	VAL	0	-0.014	-0.010	65.243	0.000	0.000	0.000	0.000	0.000	0.000
119	A	139	ASN	0	0.002	0.013	65.885	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	140	VAL	0	0.027	0.002	64.559	0.000	0.000	0.000	0.000	0.000	0.000
121	A	141	ASP	-1	-0.753	-0.855	64.301	-0.009	-0.009	0.000	0.000	0.000	0.000
122	A	142	ALA	0	-0.031	-0.010	59.221	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	143	VAL	0	0.020	-0.002	59.541	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	144	MET	0	0.009	0.021	60.627	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	145	ARG	1	1.003	1.007	58.479	0.012	0.012	0.000	0.000	0.000	0.000
126	A	146	THR	0	-0.051	-0.023	55.716	-0.001	-0.001	0.000	0.000	0.000	0.000
127	A	147	LEU	0	0.008	0.003	57.693	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	148	LEU	0	0.014	0.022	59.682	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	149	ALA	0	0.012	0.014	56.562	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	150	ARG	1	0.761	0.864	51.287	0.014	0.014	0.000	0.000	0.000	0.000
131	A	151	GLY	0	0.091	0.046	56.329	0.000	0.000	0.000	0.000	0.000	0.000
132	A	152	LEU	0	-0.064	-0.006	56.228	0.000	0.000	0.000	0.000	0.000	0.000
133	A	153	ILE	0	-0.008	-0.018	60.237	0.001	0.001	0.000	0.000	0.000	0.000
134	A	154	THR	0	0.006	-0.007	63.319	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	155	GLU	-1	-0.890	-0.949	65.949	-0.014	-0.014	0.000	0.000	0.000	0.000
136	A	156	VAL	0	-0.036	-0.007	69.354	0.000	0.000	0.000	0.000	0.000	0.000
137	A	157	GLY	0	0.050	0.004	72.029	0.000	0.000	0.000	0.000	0.000	0.000
138	A	158	THR	0	-0.030	-0.019	74.948	0.000	0.000	0.000	0.000	0.000	0.000
139	A	159	ASP	-1	-0.914	-0.915	77.458	-0.007	-0.007	0.000	0.000	0.000	0.000
140	A	160	ALA	0	-0.007	-0.001	79.884	0.000	0.000	0.000	0.000	0.000	0.000
141	A	161	ASP	-1	-0.905	-0.943	83.391	-0.007	-0.007	0.000	0.000	0.000	0.000
142	A	162	THR	0	-0.092	-0.083	80.495	0.000	0.000	0.000	0.000	0.000	0.000
143	A	163	GLY	0	0.002	0.005	80.647	0.000	0.000	0.000	0.000	0.000	0.000
144	A	164	ALA	0	-0.056	-0.025	76.179	0.000	0.000	0.000	0.000	0.000	0.000
145	A	165	VAL	0	0.012	-0.003	71.494	0.000	0.000	0.000	0.000	0.000	0.000
146	A	166	THR	0	-0.012	-0.012	73.564	0.001	0.001	0.000	0.000	0.000	0.000
147	A	167	PHE	0	-0.050	-0.037	67.403	-0.001	-0.001	0.000	0.000	0.000	0.000
148	A	168	ALA	0	0.036	0.024	68.410	0.001	0.001	0.000	0.000	0.000	0.000
149	A	169	THR	0	0.001	0.002	64.150	0.000	0.000	0.000	0.000	0.000	0.000
150	A	170	THR	0	-0.038	-0.042	61.240	0.000	0.000	0.000	0.000	0.000	0.000
151	A	171	GLU	-1	-0.834	-0.927	62.837	-0.015	-0.015	0.000	0.000	0.000	0.000
152	A	172	LEU	0	0.022	0.008	55.497	0.000	0.000	0.000	0.000	0.000	0.000
153	A	173	PHE	0	-0.064	-0.045	58.505	0.000	0.000	0.000	0.000	0.000	0.000
154	A	174	LEU	0	0.019	0.000	59.983	0.001	0.001	0.000	0.000	0.000	0.000
155	A	175	GLU	-1	-0.879	-0.931	56.947	-0.021	-0.021	0.000	0.000	0.000	0.000
156	A	176	ARG	1	0.805	0.893	52.182	0.020	0.020	0.000	0.000	0.000	0.000
157	A	177	LEU	0	-0.110	-0.011	55.388	0.001	0.001	0.000	0.000	0.000	0.000
158	A	178	GLY	0	0.017	-0.008	57.247	0.001	0.001	0.000	0.000	0.000	0.000
159	A	179	LEU	0	-0.058	-0.024	58.816	0.001	0.001	0.000	0.000	0.000	0.000
160	A	180	THR	0	0.046	0.032	61.063	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:21:ALA)